Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1
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katharina
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by katharina » Fri Nov 20, 2015 1:20 pm
Originally posted in the old forum by Fred on 21.12.2012 - 22:18
when trying to run bamtools filter -in output_directory/accepted_hits.bam -out output_directory/accepted_hits.noN.bam -script operation_N_filter.txt
I receive the following error:
bamtools filter ERROR: could not open script: operation_N_filter.txt for reading
Code: Select all
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string::_S_construct NULL not valid
Aborted (core dumped)
katharina
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Posts: 531 Joined: Wed Nov 18, 2015 6:14 pm
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by katharina » Fri Nov 20, 2015 1:20 pm
by Fred on 21.12.2012 - 22:51
bamtools filter
Is the operation_N_filter.txt script in the bamtools toolkit or is this an external script.
katharina
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Posts: 531 Joined: Wed Nov 18, 2015 6:14 pm
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by katharina » Fri Nov 20, 2015 1:20 pm
by katharina on 28.12.2012 - 17:55
This is an external script, but it has very simple contents:
Code: Select all
{
"filters" :
[
{ "id" : "operation_N",
"cigar" : "*N*"
},
{ "id" : "is_Mapped",
"isMapped" : "true"
}
],
"rule" : "!operation_N & is_Mapped"
}
katharina
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Posts: 531 Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
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by katharina » Fri Nov 20, 2015 1:21 pm
by Fred on 31.12.2012 - 00:07
Great. This is what I was looking for. Thanks!